DOCSLIB.ORG

Conserved Bacterial Genomes from Two Geographically Distinct Peritidal Stromatolite Formations Shed Light on Potential Functiona

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Conserved Bacterial Genomes from Two Geographically Distinct Peritidal Stromatolite Formations Shed Light on Potential Functiona bioRxiv preprint doi: https://doi.org/10.1101/818625; this version posted March 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Conserved bacterial genomes from two geographically distinct peritidal 2 stromatolite formations shed light on potential functional guilds 3 4 Running Title: Functional bacterial guilds in stromatolites 5 6 Samantha C. Waterwortha, Eric W. Isemongerb, Evan R. Reesa, Rosemary A. 7 Dorringtonb and Jason C. Kwana# 8 a Division of Pharmaceutical Sciences, University of Wisconsin, 777 Highland Ave., 9 Madison, Wisconsin 53705, USA 10 b Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 11 South Africa 12 #Corresponding author. Email: [email protected]; Phone: 608-262-3829 13 14 ORIGINALITY-SIGNIFICANCE 15 Peritidal stromatolites are unique among stromatolite formations as they grow at the 16 dynamic interface of calcium carbonate-rich groundwater and coastal marine waters. 17 The peritidal space forms a relatively unstable environment and the factors that 18 influence the growth of these peritidal structures is not well understood. To our 19 knowledge, this is the first comparative study that assesses species conservation within 20 the microbial communities of two geographically distinct peritidal stromatolite 21 formations. We assessed the potential functional roles of these communities using 22 genomic bins clustered from metagenomic sequencing data. We identified several 23 conserved bacterial species across the two sites and hypothesize that their genetic 1 bioRxiv preprint doi: https://doi.org/10.1101/818625; this version posted March 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 24 functional potential may be important in the formation of pertidal stromatolites. We 25 contrasted these findings against a well-studied site in Shark Bay, Australia and show 26 that, unlike these hypersaline formations, archaea do not play a major role in peritidal 27 stromatolite formation. Furthermore, bacterial nitrogen and phosphate metabolisms of 28 conserved species may be driving factors behind lithification in peritidal stromatolites. 29 30 SUMMARY 31 Stromatolites are complex microbial mats that form lithified layers and ancient forms are 32 the oldest evidence of life on earth, dating back over 3.4 billion years. Modern 33 stromatolites are relatively rare but may provide clues about the function and evolution 34 of their ancient counterparts. In this study, we focus on peritidal stromatolites occurring 35 at Cape Recife and Schoenmakerskop on the southeastern South African coastline. 36 Using assembled shotgun metagenomic data we obtained 183 genomic bins, of which 37 the most dominant taxa were from the Cyanobacteriia class (Cyanobacteria phylum), 38 with lower but notable abundances of bacteria classified as Alphaproteobacteria, 39 Gammaproteobacteria and Bacteroidia. We identified functional gene sets in bacterial 40 species conserved across two geographically distinct stromatolite formations, which 41 may promote carbonate precipitation through the reduction of nitrogenous compounds 42 and possible production of calcium ions. We propose that an abundance of extracellular 43 alkaline phosphatases may lead to the formation of phosphatic deposits within these 44 stromatolites. We conclude that the cumulative effect of several conserved bacterial 45 species drives accretion in these two stromatolite formations. 46 2 bioRxiv preprint doi: https://doi.org/10.1101/818625; this version posted March 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 47 INTRODUCTION 48 Stromatolites are organo-sedimentary structures that date back more than 3.4 billion 49 years, forming the oldest fossils of living organisms on Earth (Dupraz et al., 2009). A 50 more recent discovery of stromatolite-like structures in Greenland suggests that the 51 structures may date as far back as 3.7 - 3.8 billion years (Nutman et al., 2016), 52 however, their biogenic origin remains under debate (Witze, 2016). The emergence of 53 Cyanobacteria in stromatolites approximately 2.3 billion years ago initiated the Great 54 Oxygenation Event that fundamentally altered the Earth’s redox potential and resulted in 55 an explosion of oxygen-based and multicellular biological diversity (Soo et al., 2017). 56 Ancient stromatolites could provide insight into how microorganisms shaped early 57 eukaryotic evolution. Unfortunately ancient microbial mats are not sufficiently preserved 58 for identification of these microbes and individual bacteria cannot be classified more 59 specifically than phylum Cyanobacteria due to morphological conservatism (Awramik, 60 1992; Dupraz et al., 2009). The study of extant stromatolite analogs may therefore help 61 to elucidate the biological mechanisms that led to the formation and evolution of their 62 ancient ancestors. Modern stromatolites are formed through a complex combination of 63 both biotic and abiotic processes. The core process revolves around the carbon cycle 64 where bacteria transform inorganic carbon into bioavailable organic carbon for 65 respiration. Bacterial respiration in turn results in the release of inorganic carbon, which, 66 under alkaline conditions, will bind cations and precipitate primarily as calcium 67 carbonate (Dupraz et al., 2009). This carbonate precipitate, along with sediment grains, 68 can then become trapped within bacterial biofilms forming the characteristic lithified 69 layers. 3 bioRxiv preprint doi: https://doi.org/10.1101/818625; this version posted March 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 70 71 Alteration of the pH and subsequently, the solubility index (SI), may promote 72 mineralization or dissolution of carbonate minerals through microbial cycling of redox 73 sensitive compounds such as phosphate, nitrogen, sulfur and other nutrients within the 74 biofilm. This in turn regulates the rate of carbonate accretion and stromatolite growth. 75 Particularly, photosynthesis and sulfate reduction have been demonstrated to increase 76 alkalinity thereby promoting carbonate accretion, resulting in the gradual formation of 77 lithified mineral layers (Dupraz et al., 2009). In some stromatolite formations such as 78 those of Shark Bay, Australia, there is abundant genetic potential for both dissimilatory 79 oxidation of sulfur (which may promote dissolution under oxic conditions and 80 precipitation under anoxic conditions) and dissimilatory reduction of sulfate (which 81 promotes precipitation) (Gallagher et al., 2012; Casaburi et al., 2016; Wong et al., 82 2018). 83 84 The biogenicity of stromatolites has been studied extensively in the hypersaline and 85 marine formations of Shark Bay, Australia and Exuma Cay, Bahamas, respectively 86 (Khodadad and Foster, 2012; Babilonia et al., 2018). The presence of Archaea has 87 been noted in several microbial mat and stromatolite systems (Casaburi et al., 2016; 88 Balci et al., 2018; Medina-Chávez et al., 2019), particularly in the stromatolites of Shark 89 Bay, where they are hypothesized to potentially fulfill the role of nitrifiers and 90 hydrogenotrophic methanogens (Wong et al., 2017). Although Cyanobacteria, 91 Proteobacteria and Bacteroidetes appear to be abundant in both marine and 92 hypersaline systems, Cyanobacteria are proposed to be particularly vital to these 4 bioRxiv preprint doi: https://doi.org/10.1101/818625; this version posted March 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 93 formations through the combined effect of biofilm formation, carbon fixation, nitrogen 94 fixation and endolithic (boring) activity (Macintyre et al., 2000; Khodadad and Foster, 95 2012; Casaburi et al., 2016; Babilonia et al., 2018). 96 97 Peritidal tufa stromatolite systems are found along the southeastern coastline of South 98 Africa (SA). They are geographically isolated, occurring at coastal dune seeps 99 separated by stretches of coastline (Smith et al., 2018). In these systems, stromatolite 100 formations extend from freshwater to intertidal zones and are dominated by 101 Cyanobacteria, Bacteroidetes and Proteobacteria (Perissinotto et al., 2014). The 102 stromatolites are impacted by fluctuating environmental pressures caused by periodic 103 inundation by seawater, which affects the nutrient concentrations, temperature and 104 chemistry of the system (Rishworth et al., 2016). These formations are characterized by 105 their proximity to the ocean, where stromatolites in the upper formations receive 106 freshwater from the inflow seeps, middle formation stromatolites withstand a mix of 107 freshwater
Load more

Recommended publications
  • Reconstructing the Origin of Oxygenic Photosynthesis: Do Assembly and Photoactivation Recapitulate Evolution?
    HYPOTHESIS AND THEORY published: 02 March 2016 doi: 10.3389/fpls.2016.00257 Reconstructing the Origin of Oxygenic Photosynthesis: Do Assembly and Photoactivation Recapitulate Evolution? Tanai Cardona * Department of Life Sciences, Imperial College London, London, UK Due to the great abundance of genomes and protein structures that today span a broad diversity of organisms, now more than ever before, it is possible to reconstruct the molecular evolution of protein complexes at an incredible level of detail. Here, I recount the story of oxygenic photosynthesis or how an ancestral reaction center was transformed into a sophisticated photochemical machine capable of water oxidation. First, I review the evolution of all reaction center proteins in order to highlight that Photosystem II and Photosystem I, today only found in the phylum Cyanobacteria, branched out very early in the history of photosynthesis. Therefore, it is very unlikely that they were acquired via horizontal gene transfer from any of the described phyla of Edited by: anoxygenic phototrophic bacteria. Second, I present a new evolutionary scenario for the Julian Eaton-Rye, origin of the CP43 and CP47 antenna of Photosystem II. I suggest that the antenna University of Otago, New Zealand proteins originated from the remodeling of an entire Type I reaction center protein and Reviewed by: Anthony William Larkum, not from the partial gene duplication of a Type I reaction center gene. Third, I highlight University of Technology, Sydney, how Photosystem II and Photosystem I reaction center proteins interact with small Australia Martin Hohmann-Marriott, peripheral subunits in remarkably similar patterns and hypothesize that some of this Norwegian University of Science and complexity may be traced back to the most ancestral reaction center.
    [Show full text]
  • Community Structure and Function of High-Temperature Chlorophototrophic Microbial Mats Inhabiting Diverse Geothermal Environments
    ORIGINAL RESEARCH ARTICLE published: 03 June 2013 doi: 10.3389/fmicb.2013.00106 Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments Christian G. Klatt 1,2†,William P.Inskeep 1,2*, Markus J. Herrgard 3, Zackary J. Jay 1,2, Douglas B. Rusch4, Susannah G.Tringe 5, M. Niki Parenteau 6,7, David M. Ward 1,2, Sarah M. Boomer 8, Donald A. Bryant 9,10 and Scott R. Miller 11 1 Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA 2 Thermal Biology Institute, Montana State University, Bozeman, MT, USA 3 Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark 4 Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, USA 5 Department of Energy Joint Genome Institute, Walnut Creek, CA, USA 6 Search for Extraterrestrial Intelligence Institute, Mountain View, CA, USA 7 National Aeronautics and Space Administration Ames Research Center, Mountain View, CA, USA 8 Western Oregon University, Monmouth, OR, USA 9 Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA 10 Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA 11 Department of Biological Sciences, University of Montana, Missoula, MT, USA Edited by: Six phototrophic microbial mat communities from different geothermal springs (YNP) were Martin G. Klotz, University of North studied using metagenome sequencing and geochemical analyses. The primary goals of Carolina at Charlotte, USA this work were to determine differences in community composition of high-temperature Reviewed by: Andreas Teske, University of North phototrophic mats distributed across theYellowstone geothermal ecosystem, and to iden- Carolina at Chapel Hill, USA tify metabolic attributes of predominant organisms present in these communities that may Jesse Dillon, California State correlate with environmental attributes important in niche differentiation.
    [Show full text]
  • Optimization and Characterization of the Growth Of
    OPTIMIZATION AND CHARACTERIZATION OF THE GROWTH OF THE PHOTOSYNTHETIC BACTERIUM BLASTOCHLORIS VIRIDIS AND A BRIEF SURVEY OF ITS POTENTIAL AS A REMEDIATIVE TOOL A Dissertation Submitted to the Graduate School of the University of Notre Dame in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Darcy Danielle LaClair, B.S. ___________________________________ Agnes E. Ostafin, Director Graduate Program in Chemical and Biomolecular Engineering Notre Dame, Indiana April 2006 OPTIMIZATION AND CHARACTERIZATION OF THE GROWTH OF THE PHOTOSYNTHETIC BACTERIUM BLASTOCHLORIS VIRIDIS AND A BRIEF SURVEY OF THEIR POTENTIAL AS A REMEDIATIVE TOOL Abstract by Darcy Danielle LaClair The growth of B. viridis was characterized in an undefined rich medium and a well-defined medium, which was later selected for further experimentation to insure repeatability. This medium presented a significant problem in obtaining either multigenerational or vigorous growth because of metabolic limitations; therefore optimization of the medium was undertaken. A primary requirement to obtain good growth was a shift in the pH of the medium from 6.9 to 5.9. Once this shift was made, it was possible to obtain growth in subsequent generations, and the media formulation was optimized. A response curve suggested optimum concentrations of 75 mM carbon, supplemented as sodium malate, 12.5 mM nitrogen, supplemented as ammonium sulfate, Darcy Danielle LaClair and 12.7 mM phosphate buffer. In addition, the vitamins p-Aminobenzoic acid, Thiamine, Biotin, B12, and Pantothenate were important to achieving good growth and good pigment formation. Exogenous carbon dioxide, added as 2.5 g sodium bicarbonate per liter media also enhanced growth and reduced the lag time.
    [Show full text]
  • Investigation on the Production of Secondary Metabolites from Anoxygenic Phototrophic Bacteria
    Investigation on the production of secondary metabolites from anoxygenic phototrophic bacteria. Dissertation Zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Christian-Albrechts-Universität zu Kiel Vorgelegt von Min Sun Kiel 2015 Referent: Prof. Dr. Johannes F. Imhoff Korreferentin: Prof. Dr. Ute Hentschel-Humeida Tag der mündlichen Prüfung: 19.02.2016 Zum Druck genehmigt: Ja gez. Prof. Dr. Johannes F. Imhoff This present work was carried out at the GEOMAR Helmholtz Centre for Ocean Research Kiel Christian-Albrechts-University of Kiel from August 2011 to August 2015 under the supervision of Prof. Dr. Johannes F. Imhoff. Scientific contribution All the strains used in this studied were offered by Prof. Dr. Johannes F. Imhoff. Allochromatium vinosum strain MT86 was isolated and identified by Dr. Marcus Tank. All bioassays of crude extracts, fractions and pure compounds were done by Arlette Wenzel-Storjohann (Marine Natural Products, GEOMAR). NMR measurement was performed at the Otto-Diels Institute of Organic Chemistry (Christian-Albrechts University of Kiel) and NMR data analysis was analysis by the assistance of Dr. Bin Wu (Zhejiang University, China) and Prof. Dr. Alex Zeeck (BioViotica Naturstoffe GmbH, Götingen). Prof. Dr. Alex Zeeck did the TLC and IR, CD, and polarimetry measurements. All other experiments were done by Min Sun under supervision of Prof. Dr. Johannes F. Imhoff at GEOMAR Marine Microbiology Department. Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit unter Einhaltung der Regeln guter wissenschaftlicher Praxis der Deutschen Forschungsgesellschaft verfasst habe, und dass sie nach Form und Inhalt meine eigene Arbeit ist. Außer den angegebenen Quellen und Hilfsmitteln wurden keine weiteren verwendet.
    [Show full text]
  • Articles, Onomic Units (Otus) of Which Half Were Related to Bacteria Their Numbers Are Highly Variable in Both Time and Space
    Biogeosciences, 4, 115–124, 2007 www.biogeosciences.net/4/115/2007/ Biogeosciences © Author(s) 2007. This work is licensed under a Creative Commons License. Fluorescent pseudomonads isolated from Hebridean cloud and rain water produce biosurfactants but do not cause ice nucleation H. E. Ahern1, K. A. Walsh2, T. C. J. Hill2, and B. F. Moffett2 1University of East London, Romford Road, Stratford, London, UK 2Environment Agency, Wallingford, UK Received: 1 September 2006 – Published in Biogeosciences Discuss.: 4 October 2006 Revised: 11 January 2007 – Accepted: 9 February 2007 – Published: 12 February 2007 Abstract. Microorganisms were discovered in clouds over 1 Introduction 100 years ago but information on bacterial community struc- ture and function is limited. Clouds may not only be a niche There has been a resurgence of interest in microorganisms within which bacteria could thrive but they might also in- in the atmosphere due, in part, to heightened awareness of fluence dynamic processes using ice nucleating and cloud disease epidemiology. Health issues however may be less condensing abilities. Cloud and rain samples were collected important than their role in cloud and rainfall processes and from two mountains in the Outer Hebrides, NW Scotland, link to climate change. Recently it has been reported that UK. Community composition was determined using a com- there are between 1500 and 355 000 bacteria per millilitre of bination of amplified 16S ribosomal DNA restriction analy- cloud water (Sattler et al., 2001, Bauer et al., 2002 and Am- sis and sequencing. 256 clones yielded 100 operational tax- ato et al., 2005). Therefore, as with other aerosol particles, onomic units (OTUs) of which half were related to bacteria their numbers are highly variable in both time and space.
    [Show full text]
  • Metaproteomics Characterization of the Alphaproteobacteria
    Avian Pathology ISSN: 0307-9457 (Print) 1465-3338 (Online) Journal homepage: https://www.tandfonline.com/loi/cavp20 Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssus gallinae (De Geer, 1778) José Francisco Lima-Barbero, Sandra Díaz-Sanchez, Olivier Sparagano, Robert D. Finn, José de la Fuente & Margarita Villar To cite this article: José Francisco Lima-Barbero, Sandra Díaz-Sanchez, Olivier Sparagano, Robert D. Finn, José de la Fuente & Margarita Villar (2019) Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssusgallinae (De Geer, 1778), Avian Pathology, 48:sup1, S52-S59, DOI: 10.1080/03079457.2019.1635679 To link to this article: https://doi.org/10.1080/03079457.2019.1635679 © 2019 The Author(s). Published by Informa View supplementary material UK Limited, trading as Taylor & Francis Group Accepted author version posted online: 03 Submit your article to this journal Jul 2019. Published online: 02 Aug 2019. Article views: 694 View related articles View Crossmark data Citing articles: 3 View citing articles Full Terms & Conditions of access and use can be found at https://www.tandfonline.com/action/journalInformation?journalCode=cavp20 AVIAN PATHOLOGY 2019, VOL. 48, NO. S1, S52–S59 https://doi.org/10.1080/03079457.2019.1635679 ORIGINAL ARTICLE Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssus gallinae (De Geer, 1778) José Francisco Lima-Barbero a,b, Sandra Díaz-Sanchez a, Olivier Sparagano c, Robert D. Finn d, José de la Fuente a,e and Margarita Villar a aSaBio.
    [Show full text]
  • BIODATA 1) Name : Dr. Ch. Sasikala 2) Designation
    BIODATA 1) Name : Dr. Ch. Sasikala 2) Designation : Professor and Chairperson, Board of Studies in Environemntal Science and Technology 3) Address a) Official : Centre for Environment, IST, JNT University Hyderabad, Kukatpally, Hyderabad – 500 085 INDIA Phone: 040-23158661 /2/3/4 Extn.3480 Email: [email protected] [email protected] , [email protected] b) Home : 5-3-357, Rashtrapathi Road, Secunderabad 500 003 INDIA Phone: Res. 040-27535462 (R) Mobile : 9000796341 4) Date of Birth : 9 th March 1963 5) Nature of work : Teaching/Research 6) Research experience : 30 years of research experience Including 26 years of post-doctoral experience 7) PG teaching experience : 21 years 8) Field of specialization : Environmental microbiology and biotechnology (Bacterial diversity, Bioprospecting, biodegradation and Bioremediation) 9) Research publications : 191 (Annexure A) (In standard refereed journals) Cumulative impact factor: 440 h index: 28; Number of citations: ~3,000 1 10) Academic qualifications and career record: a) Degrees : B.Sc., B.Ed., M.Sc., Ph.D. b) Details of Educational qualifications : Exam Subjects Board/ Year of Class/ % of passed University passing Division Marks S.S.C Tel. Hindi, Board of 1978 I 70 Eng. Maths, Secondary Ed. Gen. Sci. and Andhra Social studies Pradesh Intermediate Biol. Phy. Board of 1980 I 76.5 Chem. Intermediate Education, A.P B.Sc. Bot. Chem. Osmania 1983 I 83.2 Microbiol University B.Ed. Life Sciences Osmania 1984 I 68 University M.Sc. Applied Bharathiar 1986 I 70 Microbiology University (university second
    [Show full text]
  • A Microbiotic Survey of Lichen-Associated Bacteria Reveals a New Lineage from the Rhizobiales
    SYMBIOSIS (2009) 49, 163–180 ©Springer Science+Business Media B.V. 2009 ISSN 0334-5114 A microbiotic survey of lichen-associated bacteria reveals a new lineage from the Rhizobiales Brendan P. Hodkinson* and François Lutzoni Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA, Tel. +1-443-340-0917, Fax. +1-919-660-7293, Email. [email protected] (Received June 10, 2008; Accepted November 5, 2009) Abstract This study uses a set of PCR-based methods to examine the putative microbiota associated with lichen thalli. In initial experiments, generalized oligonucleotide-primers for the 16S rRNA gene resulted in amplicon pools populated almost exclusively with fragments derived from lichen photobionts (i.e., Cyanobacteria or chloroplasts of algae). This effectively masked the presence of other lichen-associated prokaryotes. In order to facilitate the study of the lichen microbiota, 16S ribosomal oligonucleotide-primers were developed to target Bacteria, but exclude sequences derived from chloroplasts and Cyanobacteria. A preliminary microbiotic survey of lichen thalli using these new primers has revealed the identity of several bacterial associates, including representatives of the extremophilic Acidobacteria, bacteria in the families Acetobacteraceae and Brucellaceae, strains belonging to the genus Methylobacterium, and members of an undescribed lineage in the Rhizobiales. This new lineage was investigated and characterized through molecular cloning, and was found to be present in all examined lichens that are associated with green algae. There is evidence to suggest that members of this lineage may both account for a large proportion of the lichen-associated bacterial community and assist in providing the lichen thallus with crucial nutrients such as fixed nitrogen.
    [Show full text]
  • Starkeya Novella Type Strain (ATCC 8093T) Ulrike Kappler1, Karen Davenport2, Scott Beatson1, Susan Lucas3, Alla Lapidus3, Alex Copeland3, Kerrie W
    Standards in Genomic Sciences (2012) 7:44-58 DOI:10.4056/sigs.3006378 Complete genome sequence of the facultatively chemolithoautotrophic and methylotrophic alpha Proteobacterium Starkeya novella type strain (ATCC 8093T) Ulrike Kappler1, Karen Davenport2, Scott Beatson1, Susan Lucas3, Alla Lapidus3, Alex Copeland3, Kerrie W. Berry3, Tijana Glavina Del Rio3, Nancy Hammon3, Eileen Dalin3, Hope Tice3, Sam Pitluck3, Paul Richardson3, David Bruce2,3, Lynne A. Goodwin2,3, Cliff Han2,3, Roxanne Tapia2,3, John C. Detter2,3, Yun-juan Chang3,4, Cynthia D. Jeffries3,4, Miriam Land3,4, Loren Hauser3,4, Nikos C. Kyrpides3, Markus Göker5, Natalia Ivanova3, Hans-Peter Klenk5, and Tanja Woyke3 1 The University of Queensland, Brisbane, Australia 2 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 3 DOE Joint Genome Institute, Walnut Creek, California, USA 4 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 5Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany *Corresponding author(s): Hans-Peter Klenk ([email protected]) and Ulrike Kappler ([email protected]) Keywords: strictly aerobic, facultatively chemoautotrophic, methylotrophic and heterotrophic, Gram-negative, rod-shaped, non-motile, soil bacterium, Xanthobacteraceae, CSP 2008 Starkeya novella (Starkey 1934) Kelly et al. 2000 is a member of the family Xanthobacteraceae in the order ‘Rhizobiales’, which is thus far poorly characterized at the genome level. Cultures from this spe- cies are most interesting due to their facultatively chemolithoautotrophic lifestyle, which allows them to both consume carbon dioxide and to produce it. This feature makes S. novella an interesting model or- ganism for studying the genomic basis of regulatory networks required for the switch between con- sumption and production of carbon dioxide, a key component of the global carbon cycle.
    [Show full text]
  • Rhodopseudomonas Viridis and Rhodopseudomonas Sulfoviridis to the Genus Blastochloris Gen
    INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1997, p. 217-219 Vol. 47, No. 1 0020-7713/97/$04.00+ 0 Copyright 0 1997, International Union of Microbiological Societies Transfer of the Bacteriochlorophyll &Containing Phototrophic Bacteria Rhodopseudomonas viridis and Rhodopseudomonas sulfoviridis to the Genus Blastochloris gen. nov. AKIRA HIMISHI* Department of Ecological Engineering, Toyohashi University of Technology, Toyohashi 441, and Laboratory of Environmental Biotechnology, Konishi Co., Tokyo 130, Japan The phylogenetic positions of the bacteriochlorophyll (BChl) b-producing budding phototrophic bacteria Rhodopseudomonas viridis and Rhodopseudomonas sulfoviridis were studied on the basis of 16s rRNA gene sequence information. These bacteria formed a tight cluster with the genus Rhodoplanes as a sister group within the alpha-2 subgroup of the Proteobacteria. Genomic DNA-DNA hybridization assays showed that R. viridis and R. sulfoviridis were closely related but were different species. Creation of the genus Blastochloris gen. nov. is proposed to accommodate these BChl b-producing species of phototrophic bacteria. In 1984 some species of the classically defined genus Rho- tion of the organisms. For Rhodopseudomonas sulfoviridis, the dopseudomonas were reclassified into new genera, including medium was supplemented with 10 mM glucose, 2 mM sodium the new genera Rhodobacter and Rhodopila, on the basis of sulfide (neutralized), and 2 mM thiosulfate. The medium was modern taxonomic criteria (17). In recent years, the taxonomy supplemented with 10 mM pyruvate (filter sterilized) for Rho- of the genus Rhodopseudomonas has been further reevaluated doplanes roseus. The organisms were grown at 30°C in screw- on the basis of increasing molecular and chemotaxonomic in- cap test tubes under anaerobic conditions in the light.
    [Show full text]
  • Photosynthesis Is Widely Distributed Among Proteobacteria As Demonstrated by the Phylogeny of Puflm Reaction Center Proteins
    fmicb-08-02679 January 20, 2018 Time: 16:46 # 1 ORIGINAL RESEARCH published: 23 January 2018 doi: 10.3389/fmicb.2017.02679 Photosynthesis Is Widely Distributed among Proteobacteria as Demonstrated by the Phylogeny of PufLM Reaction Center Proteins Johannes F. Imhoff1*, Tanja Rahn1, Sven Künzel2 and Sven C. Neulinger3 1 Research Unit Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany, 2 Max Planck Institute for Evolutionary Biology, Plön, Germany, 3 omics2view.consulting GbR, Kiel, Germany Two different photosystems for performing bacteriochlorophyll-mediated photosynthetic energy conversion are employed in different bacterial phyla. Those bacteria employing a photosystem II type of photosynthetic apparatus include the phototrophic purple bacteria (Proteobacteria), Gemmatimonas and Chloroflexus with their photosynthetic relatives. The proteins of the photosynthetic reaction center PufL and PufM are essential components and are common to all bacteria with a type-II photosynthetic apparatus, including the anaerobic as well as the aerobic phototrophic Proteobacteria. Edited by: Therefore, PufL and PufM proteins and their genes are perfect tools to evaluate the Marina G. Kalyuzhanaya, phylogeny of the photosynthetic apparatus and to study the diversity of the bacteria San Diego State University, United States employing this photosystem in nature. Almost complete pufLM gene sequences and Reviewed by: the derived protein sequences from 152 type strains and 45 additional strains of Nikolai Ravin, phototrophic Proteobacteria employing photosystem II were compared. The results Research Center for Biotechnology (RAS), Russia give interesting and comprehensive insights into the phylogeny of the photosynthetic Ivan A. Berg, apparatus and clearly define Chromatiales, Rhodobacterales, Sphingomonadales as Universität Münster, Germany major groups distinct from other Alphaproteobacteria, from Betaproteobacteria and from *Correspondence: Caulobacterales (Brevundimonas subvibrioides).
    [Show full text]
  • Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota
    University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln US Department of Energy Publications U.S. Department of Energy 2010 Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota Gurdeep Rastogi South Dakota School of Mines and Technology Shariff Osman Lawrence Berkeley National Laboratory Ravi K. Kukkadapu Pacific Northwest National Laboratory, [email protected] Mark Engelhard Pacific Northwest National Laboratory Parag A. Vaishampayan California Institute of Technology See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/usdoepub Part of the Bioresource and Agricultural Engineering Commons Rastogi, Gurdeep; Osman, Shariff; Kukkadapu, Ravi K.; Engelhard, Mark; Vaishampayan, Parag A.; Andersen, Gary L.; and Sani, Rajesh K., "Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota" (2010). US Department of Energy Publications. 170. https://digitalcommons.unl.edu/usdoepub/170 This Article is brought to you for free and open access by the U.S. Department of Energy at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in US Department of Energy Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Gurdeep Rastogi, Shariff Osman, Ravi K. Kukkadapu, Mark Engelhard, Parag A. Vaishampayan, Gary L. Andersen, and Rajesh K. Sani This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/ usdoepub/170 Microb Ecol (2010) 60:539–550 DOI 10.1007/s00248-010-9657-y SOIL MICROBIOLOGY Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota Gurdeep Rastogi & Shariff Osman & Ravi Kukkadapu & Mark Engelhard & Parag A.
    [Show full text]